[ Started: 2025-08-04 19:59:51 CEST ] [ liana v0.1.14 for BioC-3.22 from https://github.com/saezlab/liana@master (6cab46c 2024-08-07 08:58:01) ] [1] "Libraries: " "/home/omnipath/local/R/4.5-3.22" [3] "/home/omnipath/local/R/4.5" "/usr/lib/R/library" 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.22 (BiocManager 1.30.26), R 4.5.1 (2025-06-13) Old packages: 'dorothea' trying URL 'https://bioconductor.org/packages/3.22/data/experiment/src/contrib/dorothea_1.21.0.tar.gz' Content type 'application/x-gzip' length 34711252 bytes (33.1 MB) ================================================== downloaded 33.1 MB * installing *source* package ‘dorothea’ ... ** this is package ‘dorothea’ version ‘1.21.0’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (dorothea) The downloaded source packages are in ‘/tmp/Rtmp6y2ZLQ/downloaded_packages’ 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.22 (BiocManager 1.30.26), R 4.5.1 (2025-06-13) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' CellChat (NA -> e4f68625b...) [GitHub] OmnipathR (3.17.4 -> a7f3b9dda...) [GitHub] decoupleR (2.15.0 -> ee886864d...) [GitHub] BiocNeigh... (NA -> 2.2.0 ) [CRAN] bluster (NA -> 1.18.0 ) [CRAN] scater (NA -> 1.36.0 ) [CRAN] scran (NA -> 1.36.0 ) [CRAN] Downloading GitHub repo sqjin/CellChat@HEAD Skipping 4 packages not available: Biobase, BiocNeighbors, BiocGenerics, ComplexHeatmap ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/Rtmp6y2ZLQ/remotes168d2c14b23b0f/sqjin-CellChat-e4f6862/DESCRIPTION’ ... OK * preparing ‘CellChat’: * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘CellChat_1.6.1.tar.gz’ ERROR: dependency ‘BiocNeighbors’ is not available for package ‘CellChat’ Perhaps try a variation of: install.packages('BiocNeighbors') * removing ‘/home/omnipath/local/R/4.5-3.22/CellChat’ Skipping 33 packages ahead of CRAN: UCSC.utils, Biobase, XVector, GenomeInfoDb, SparseArray, S4Arrays, IRanges, MatrixGenerics, DelayedArray, GenomicRanges, BiocGenerics, S4Vectors, SummarizedExperiment, Biostrings, KEGGREST, AnnotationDbi, BiocVersion, BiocFileCache, AnnotationHub, dir.expiry, assorthead, beachmat, ScaledMatrix, BiocParallel, SingleCellExperiment, ExperimentHub, BiocSingular, scuttle, metapod, edgeR, muscData, BiocStyle, ComplexHeatmap Installing 4 packages: BiocNeighbors, bluster, scater, scran trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/BiocNeighbors_2.2.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/bluster_1.18.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/scater_1.36.0.tar.gz' trying URL 'https://bioconductor.org/packages/3.21/bioc/src/contrib/scran_1.36.0.tar.gz' * installing *source* package ‘BiocNeighbors’ ... ** this is package ‘BiocNeighbors’ version ‘2.2.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++17 g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I../inst/include -I'/home/omnipath/local/R/4.5-3.22/Rcpp/include' -I'/home/omnipath/local/R/4.5-3.22/assorthead/include' -fpic -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/build/r-base-wwoKA3/r-base-4.5.1=/usr/src/r-base-4.5.1-1.2404.0 -Wdate-time -D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: ../inst/include/BiocNeighbors.h:23:48: error: wrong number of template arguments (3, should be 2) 23 | typedef knncolle::SimpleMatrix SimpleMatrix; | ^ In file included from /home/omnipath/local/R/4.5-3.22/assorthead/include/knncolle/Builder.hpp:5, from /home/omnipath/local/R/4.5-3.22/assorthead/include/knncolle/knncolle.hpp:4, from ../inst/include/BiocNeighbors.h:6: /home/omnipath/local/R/4.5-3.22/assorthead/include/knncolle/Matrix.hpp:128:20: note: provided for ‘template class knncolle::SimpleMatrix’ 128 | class SimpleMatrix final : public Matrix { | ^~~~~ ../inst/include/BiocNeighbors.h:28:47: error: wrong number of template arguments (2, should be at least 3) 28 | typedef knncolle::Builder Builder; | ^ /home/omnipath/local/R/4.5-3.22/assorthead/include/knncolle/Builder.hpp:28:7: note: provided for ‘template class knncolle::Builder’ 28 | class Builder { | ^~~~~~~ make: *** [/usr/lib/R/etc/Makeconf:211: RcppExports.o] Error 1 ERROR: compilation failed for package ‘BiocNeighbors’ * removing ‘/home/omnipath/local/R/4.5-3.22/BiocNeighbors’ ERROR: dependency ‘BiocNeighbors’ is not available for package ‘bluster’ Perhaps try a variation of: install.packages('BiocNeighbors') * removing ‘/home/omnipath/local/R/4.5-3.22/bluster’ ERROR: dependency ‘BiocNeighbors’ is not available for package ‘scater’ Perhaps try a variation of: install.packages('BiocNeighbors') * removing ‘/home/omnipath/local/R/4.5-3.22/scater’ ERROR: dependency ‘bluster’ is not available for package ‘scran’ Perhaps try a variation of: install.packages('bluster') * removing ‘/home/omnipath/local/R/4.5-3.22/scran’ The downloaded source packages are in ‘/tmp/Rtmp6y2ZLQ/downloaded_packages’ Downloading GitHub repo sqjin/CellChat@HEAD Skipping 4 packages not available: Biobase, BiocNeighbors, BiocGenerics, ComplexHeatmap ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/Rtmp6y2ZLQ/remotes168d2c137efee/sqjin-CellChat-e4f6862/DESCRIPTION’ ... OK * preparing ‘CellChat’: * checking DESCRIPTION meta-information ... OK * cleaning src * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * building ‘CellChat_1.6.1.tar.gz’ ERROR: dependency ‘BiocNeighbors’ is not available for package ‘CellChat’ Perhaps try a variation of: install.packages('BiocNeighbors') * removing ‘/home/omnipath/local/R/4.5-3.22/CellChat’ Downloading GitHub repo saezlab/OmnipathR@HEAD ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/Rtmp6y2ZLQ/remotes168d2c79123d02/saezlab-OmnipathR-a7f3b9d/DESCRIPTION’ ... OK * preparing ‘OmnipathR’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories Removed empty directory ‘OmnipathR/.github’ * looking to see if a ‘data/datalist’ file should be added * building ‘OmnipathR_3.17.4.tar.gz’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.17.4’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2025-08-04 20:01:07] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2025-08-04 20:01:07] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-04 20:01:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-04 20:01:07] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-08-04 20:01:07] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-08-04 18:00:56 UTC; omnipath [2025-08-04 20:01:07] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-08-04 20:01:07] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-04 18:00:57 UTC; unix [2025-08-04 20:01:07] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-04 20:01:07] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-08-04 20:01:08] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-08-04; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-08-04 20:01:08] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-08-04 20:01:08] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-04); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-04 20:01:08] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-08-04 20:01:08] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-04 20:01:08] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-08-04 20:01:08] [TRACE] [OmnipathR] Contains 1 files. [2025-08-04 20:01:08] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-04 20:01:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-04 20:01:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-04 20:01:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-08-04 20:01:08] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-08-04 20:01:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-04 20:01:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-04 20:01:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-04 20:01:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-04 20:01:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-04 20:01:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-04 20:01:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-04 20:01:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-04 20:01:08] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-08-04 20:01:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-04 20:01:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-04 20:01:09] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2025-08-04 20:01:09] [INFO] [OmnipathR] Package `OmnipathR` packaged: 2025-08-04 18:00:56 UTC; omnipath [2025-08-04 20:01:09] [INFO] [OmnipathR] Package `OmnipathR` date/publication: NA [2025-08-04 20:01:09] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-04 18:00:57 UTC; unix [2025-08-04 20:01:09] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-04 20:01:09] [INFO] [OmnipathR] Package `OmnipathR` repository: NA [2025-08-04 20:01:09] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=en_GB; collate=C; ctype=en_GB.UTF-8; tz=Europe/Berlin; date=2025-08-04; pandoc=3.1.3 @ /usr/bin/ (via rmarkdown); quarto=NA] [2025-08-04 20:01:09] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-08-04 20:01:09] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-04); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-04 20:01:09] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-08-04 20:01:09] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-04 20:01:09] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2025-08-04 20:01:09] [TRACE] [OmnipathR] Contains 1 files. [2025-08-04 20:01:09] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-04 20:01:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-04 20:01:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-04 20:01:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2025-08-04 20:01:09] [TRACE] [OmnipathR] Pandoc version: `3.1.3`. [2025-08-04 20:01:09] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-04 20:01:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-04 20:01:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-04 20:01:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-04 20:01:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-04 20:01:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-04 20:01:10] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.5-3.22/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-04 20:01:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-04 20:01:10] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR) Downloading GitHub repo saezlab/decoupleR@HEAD Skipping 1 packages ahead of CRAN: BiocParallel ── R CMD build ───────────────────────────────────────────────────────────────── * checking for file ‘/tmp/Rtmp6y2ZLQ/remotes168d2c1eee364f/saezlab-decoupleR-ee88686/DESCRIPTION’ ... OK * preparing ‘decoupleR’: * checking DESCRIPTION meta-information ... OK * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories Omitted ‘LazyData’ from DESCRIPTION * building ‘decoupleR_2.9.7.tar.gz’ * installing *source* package ‘decoupleR’ ... ** this is package ‘decoupleR’ version ‘2.9.7’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (decoupleR) Warning messages: 1: In i.p(...) : installation of package ‘/tmp/Rtmp6y2ZLQ/file168d2caf29dda/CellChat_1.6.1.tar.gz’ had non-zero exit status 2: In i.p(...) : installation of package ‘BiocNeighbors’ had non-zero exit status 3: In i.p(...) : installation of package ‘bluster’ had non-zero exit status 4: In i.p(...) : installation of package ‘scater’ had non-zero exit status 5: In i.p(...) : installation of package ‘scran’ had non-zero exit status 6: In i.p(...) : installation of package ‘/tmp/Rtmp6y2ZLQ/file168d2c26e229cb/CellChat_1.6.1.tar.gz’ had non-zero exit status [ Finished: 2025-08-04 20:01:17 CEST ]